Revision history for Perl extension App-Egaz

0.2.9 2024-12-07T12:05:28Z

    - Remove dependencies on the `fasops` executable
    - Remove --rawphylow from `egaz template`
    - `spanr` is now generating .json instead of .yml

0.2.6 2022-03-25T19:33:02Z

    - Move `egaz plottree` to `plotr tree`
    - Remove `egaz masked`, use `faops masked` instead
    - Move tt2 to share/
    - `egaz template`
        - Add `--mash`
        - Add `--fasttree`
        - Apply `nw_order` to trees

0.2.5 2020-03-06T19:07:31Z

    - `egaz template`
        - Use `samtools faidx` to replace `faops region`

0.2.4 2019-09-03T17:49:53Z

    - `egaz template`
        - Use `linkr` from `intspan` to replace `rangeops` and `jrange`
        - Use `spanr` from `intspan` to replace `runlist` and `jrunlist`

0.2.3 2019-01-26T19:01:57Z

    - `egaz plottree`
        - Some spaces above the scale bar

0.2.2 2018-11-26T17:46:32Z

    - `egaz template`
        - Add `--partition`
        - Avoid errors of too many highlights
        - Remove link4
        - Use more jrunlist and jrange
    - `egaz lpcnam`
        - Use `pigz` if available

0.2.1 2018-06-29T11:18:45Z

    - Handle old NCBI fasta headers: `>gi|\d+gb|\d+` or `>gi|\d+ref|\d+`
    - Update flowcharts
    - `egaz template`
        - Add --order
        - Exclude _fasta/ and _raw/

0.2.0 2018-04-24T21:32:24Z

    - `egaz template`
        - Add 7_multi_aligndb.sh
        - Add 7_self_aligndb.sh
        - Add 9_pack_up.sh
        - Store anno.yml and chr_length.csv to Results/
    - `egaz repeatmasker`
        - Try harder to find rmOutToGFF3.pl
    - `egaz prepseq`
        - Simplify headers for sequences in directory
    - `egaz masked`
        - Handle unmasked sequences

0.1.3 2018-04-22T20:03:24Z

    - `egaz template`
        - Add 0_prep.sh
        - and companion options
    - `egaz repeatmasker`
        - Masked files always with suffix of .fa
        - Find rmOutToGFF3.pl and create .rm.gff

0.1.2 2018-04-16T19:39:57Z

    - Create chr.fasta and chr.fasta.fai in `egaz prepseq`
    - Add `egaz fas2vcf`
    - `egaz template`
        - Fix --taxon
        - Symlink chr.fasta in 3_proc_cmd.sh
        - Add 4_vcf.sh
        - Add 4_circos.sh
        - Add prebuilt karyotype files
        - Add 7_chr_length.sh
    - Add optional dependencies

0.1.1 2018-04-15T18:21:46Z

    - Add `egaz blastmatch`
    - Add `egaz blastlink`
    - `egaz template`
        - Add 1_self_cmd.sh
        - Add 3_proc_cmd.sh

0.1.0 2018-04-14T21:55:22Z

    - Add `egaz template`
        - Add --outdir, --taxon
        - Add 1_pair_cmd.sh
        - Add 2_rawphylo.sh
        - Add 3_multi_cmd.sh
    - Add `egaz repeatmasker`
    - Add --about, --repeatmasker, --min, and --gi to `egaz prepseq`
    - `egaz raxml` supports one or more infiles
    - Requires pigz

0.0.14 2018-04-02T20:22:09Z

    - Add `egaz multiz`
    - Add normalize section to `egaz lastz`
    - Add `share/check_dep.sh`
    - Update README
    - Install multiz to $HOME/bin on CI
    - Add ladder() to Common.pm

0.0.13 2018-04-01T17:32:38Z

    - Add `egaz prepseq`
    - Add `egaz lpcnam`
    - Install lastz, faops and kent-tools to $HOME/bin on CI

0.0.12 2018-03-30T12:11:11Z

    - Add `egaz lastz`
    - Use `abstract()` to replace `use constant abstract =>`

0.0.11 2018-03-28T00:36:36Z

    - Add `egaz plottree`
    - Test installations of R and its packages
    - Add `egaz blastn`

0.0.10 2018-03-26T14:26:50Z

    - Add `egaz raxml`
    - Add exec_cmd() to Common.pm

0.0.9 2018-03-24T22:16:24Z

    - Add `egaz exactmatch`
    - Add run_sparsemem() and get_size() to Common.pm

0.0.8 2018-03-24T17:32:15Z

    - Move `egaz mergecsv` to `fasops mergecsv`
    - Escape braces in regex
    - Add overlap_ranges() to Common.pm
    - Add `egaz partition`
    - Add `egaz normalize`

0.0.7 2018-03-18T16:00:35Z

    - Add `egaz masked`
    - Use `fasops check` in t/04-lav2axt.t

0.0.6 2018-03-18T13:28:34Z

    - Add `egaz maskfasta`
    - Use markdown syntax in formats.pm

0.0.5 2018-03-18T11:57:35Z

    - Add `egaz formats`

0.0.4 2018-03-18T08:54:47Z

    - Add `egaz lav2psl`
    - Add round() to Common.pm

0.0.3 2018-03-17T08:18:33Z

    - Add `egaz lav2axt`
    - Add resolve_file() to Common.pm

0.0.2 2018-03-16T07:14:30Z

    - Add `egaz mergecsv`

0.0.1 2018-03-15T20:54:33Z

    - original version